Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003116.1 Hibiscus syriacus cultivar Beakdansim tig00006523_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 107654
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:2399 original size:18 final size:18
Alignment explanation
Indices: 2376--2420 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2366 CTGTTGTGCA
2376 TATTCTTTGCCGATGAAC
1 TATTCTTTGCCGATGAAC
*
2394 TATTCTTTGCCGATGACC
1 TATTCTTTGCCGATGAAC
2412 TATT-TTTGC
1 TATTCTTTGC
2421 TCTCTGAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (18 bp):
TATTCTTTGCCGATGAAC
Found at i:16065 original size:6 final size:5
Alignment explanation
Indices: 16052--16196 Score: 65
Period size: 5 Copynumber: 28.0 Consensus size: 5
16042 GAAAAATGAT
* *
16052 GAAAA -AAAT GAAAA GAAAA -AAGGAA GAAAA GGAAAA -ATAA -AAAA
1 GAAAA GAAAA GAAAA GAAAA GAA--AA GAAAA -GAAAA GAAAA GAAAA
16096 -AAAA GAAAAA GAAAA -AATGAA GAAAA GAAAA GAAAA GAAAA -AATGAA
1 GAAAA G-AAAA GAAAA GAA--AA GAAAA GAAAA GAAAA GAAAA GAA--AA
* *
16143 -AAATA -AAAA GAAAA TAAAAA GAAGAA GAAGAA GAAAA TGAAAAA AAAAA
1 GAAA-A GAAAA GAAAA -GAAAA GAA-AA GAA-AA GAAAA -G-AAAA GAAAA
16192 GAAAA
1 GAAAA
16197 AGTGAAAAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 36
0.72 0.05 0.23
Matches are distributed among these distances:
4 21 0.18
5 51 0.45
6 34 0.30
7 8 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (5 bp):
GAAAA
Found at i:16081 original size:23 final size:22
Alignment explanation
Indices: 16055--16235 Score: 109
Period size: 23 Copynumber: 7.7 Consensus size: 22
16045 AAATGATGAA
*
16055 AAAAATGAAAAGAAAAAAGGAAG
1 AAAAA-GAAAAGAAAAAAAGAAG
* * *
16078 AAAAGGAAAAATAAAAAAAAAAG
1 AAAAAG-AAAAGAAAAAAAGAAG
*
16101 AAAAAGAAAA-AATGAAGAA-AAG
1 AAAAAGAAAAGAA--AAAAAGAAG
* *
16123 -AAAAGAAAAGAAAAAATGAAAA
1 AAAAAGAAAAGAAAAAAAG-AAG
*
16145 ATAAAAAGAAAATAAAAAGAAGAAG
1 A-AAAA-GAAAAGAAAAA-AAGAAG
* *
16170 AAGAAGAAAATGAAAAAAAAAAG
1 AAAAAGAAAA-GAAAAAAAGAAG
16193 AAAAAGTGAAAA-AAGAAGAAAGAAG
1 AAAAA--GAAAAGAA-AA-AAAGAAG
16218 AAAGAAGAAAGAGAAAAA
1 AAA-AAGAAA-AGAAAAA
16236 TATAAAATAA
Statistics
Matches: 123, Mismatches: 17, Indels: 35
0.70 0.10 0.20
Matches are distributed among these distances:
20 3 0.02
21 11 0.09
22 12 0.10
23 42 0.34
24 19 0.15
25 30 0.24
26 6 0.05
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAAAGAAG
Found at i:16111 original size:39 final size:39
Alignment explanation
Indices: 16053--16191 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 39
16043 AAAAATGATG
16053 AAAAAAATG-AAAAGAAAAAAGGAAGAAAAGGAAAA-ATAA
1 AAAAAAATGAAAAAGAAAAAAGGAAGAAAA-GAAAAGA-AA
* *
16092 AAAAAAAAGAAAAAGAAAAAATGAAGAAAAGAAAAGAAA
1 AAAAAAATGAAAAAGAAAAAAGGAAGAAAAGAAAAGAAA
* * * *
16131 AGAAAAAATGAAAAA-TAAAAAGAAAATAAAAAGAAGAAGAAG
1 A-AAAAAATGAAAAAGAAAAAAG-GAA-GAAAAGAA-AAGAAA
*
16173 AAGAAAATGAAAAA-AAAAA
1 AAAAAAATGAAAAAGAAAAA
16192 GAAAAAGTGA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
39 21 0.25
40 34 0.40
41 23 0.27
42 6 0.07
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (39 bp):
AAAAAAATGAAAAAGAAAAAAGGAAGAAAAGAAAAGAAA
Found at i:16163 original size:41 final size:40
Alignment explanation
Indices: 16125--16253 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 40
16115 AAGAAAAGAA
16125 AAGAA-AAGAA-AAAATGAAAAATAAAAAGAAAATAAAAAG
1 AAGAAGAAGAAGAAAATGAAAAA-AAAAAGAAAATAAAAAG
*
16164 AAGAAGAAGAAGAAAATGAAAAAAAAAAGAAAAAGTGAAAA-
1 AAGAAGAAGAAGAAAATGAAAAAAAAAAG-AAAA-TAAAAAG
* * *
16205 AAGAAGAAAGAAGAAAGAAGAAAGAGAAAAATATAAAATAAAAAA
1 AAGAAG-AAGAAGAAA-ATGAAA-A-AAAAA-AGAAAATAAAAAG
16250 AAGA
1 AAGA
16254 GAAAATAAAG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 5 0.07
40 11 0.14
41 21 0.28
42 14 0.18
43 5 0.07
44 6 0.08
45 13 0.17
46 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (40 bp):
AAGAAGAAGAAGAAAATGAAAAAAAAAAGAAAATAAAAAG
Found at i:16186 original size:92 final size:94
Alignment explanation
Indices: 16032--16248 Score: 236
Period size: 92 Copynumber: 2.3 Consensus size: 94
16022 TATTTCGATT
* * * * *
16032 GAAGAAAAATGAAAAATGATGAAA-AAAATGAAAAGAAAAAAGGAAGAAAAGGAAAAATAAAAAA
1 GAAGAAAGA-GAAAAAT-ATAAAATAAAAAGAAAA-TAAAAAGGAAGAAAAGAAAAAATAAAAAA
16096 AAAAGAAAAA-GAAAAAATGAAG-AA-AAG-AA
63 AAAAGAAAAAGGAAAAAA-GAAGAAAGAAGAAA
16125 -AAGAAA-AGAAAAA-ATGAAAAATAAAAAGAAAATAAAAA-GAAGAAGAAGAAGAAAATGAAAA
1 GAAGAAAGAGAAAAATAT--AAAATAAAAAGAAAATAAAAAGGAAGAA-AAGAA-AAAAT-AAAA
16186 AAAAAAGAAAAAGTGAAAAAAGAAGAAAGAAGAAA
61 AAAAAAGAAAAAG-GAAAAAAGAAGAAAGAAGAAA
16221 GAAGAAAGAGAAAAATATAAAATAAAAA
1 GAAGAAAGAGAAAAATATAAAATAAAAA
16249 AAAGAGAAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 24
0.79 0.03 0.18
Matches are distributed among these distances:
88 2 0.02
89 6 0.06
90 18 0.17
91 15 0.14
92 22 0.21
93 4 0.04
94 9 0.08
95 3 0.03
96 2 0.02
97 16 0.15
98 7 0.07
99 2 0.02
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (94 bp):
GAAGAAAGAGAAAAATATAAAATAAAAAGAAAATAAAAAGGAAGAAAAGAAAAAATAAAAAAAAA
AGAAAAAGGAAAAAAGAAGAAAGAAGAAA
Found at i:16214 original size:7 final size:7
Alignment explanation
Indices: 16164--16233 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
16154 AAATAAAAAG
16164 AAGAAG-
1 AAGAAGA
16170 AAGAAGA
1 AAGAAGA
*
16177 AA-ATGA
1 AAGAAGA
* *
16183 AAAAAAA
1 AAGAAGA
16190 AAGAA-A
1 AAGAAGA
*
16196 AAGTGAAAA
1 AA--GAAGA
16205 AAGAAGA
1 AAGAAGA
16212 AAGAAGA
1 AAGAAGA
16219 AAGAAGA
1 AAGAAGA
16226 AAG-AGA
1 AAGAAGA
16232 AA
1 AA
16234 AATATAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
6 19 0.35
7 29 0.54
8 3 0.06
9 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (7 bp):
AAGAAGA
Found at i:16248 original size:58 final size:60
Alignment explanation
Indices: 16095--16262 Score: 76
Period size: 66 Copynumber: 2.6 Consensus size: 60
16085 AAAATAAAAA
* * * * *
16095 AAAAAGAAAAAGAAAAAATGAAGAAA-AGAAAAGAAAAGAAAAAATGAAAAATAAAAAGAAAATA
1 AAAAA-AAAAAGAAAAAATGAA-AAATA-AAAAGAAAA-TAAAAA-GAAGAAGAAGAAGAAAATG
*
16159 AAAAGAAGAAGAAGAAGAAAATGAAAAA-AAAAAGAAAAAGTGAAAA-AAGAAGAAAGAAGAAAG
1 AAAA-AA-AA-AAGAA-AAAATGAAAAATAAAAAG-AAAA-TAAAAAGAAGAAG-AAGAAGAAA-
*
16222 AAG
58 ATG
* * * *
16225 AAAGAGAAAAATATAAAAT-AAAAA-AAAGAGAAAATAAA
1 AAA-AAAAAAAGAAAAAATGAAAAATAAAAAGAAAATAAA
16263 GGGGGCTCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
60 3 0.04
61 4 0.05
62 10 0.12
63 5 0.06
64 12 0.14
65 18 0.21
66 23 0.27
67 9 0.11
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (60 bp):
AAAAAAAAAAGAAAAAATGAAAAATAAAAAGAAAATAAAAAGAAGAAGAAGAAGAAAATG
Found at i:16250 original size:16 final size:16
Alignment explanation
Indices: 16085--16262 Score: 65
Period size: 16 Copynumber: 10.5 Consensus size: 16
16075 AAGAAAAGGA
*
16085 AAAATAAAAAAAAAAG
1 AAAATAAAAAAAAGAG
*
16101 AAAA-AGAAAAAATGAAG
1 AAAATA-AAAAAAAG-AG
* *
16118 AAAAGAAAAGAAAAGAA
1 AAAATAAAA-AAAAGAG
*
16135 AAAATGAAAAATAAAAAG
1 AAAAT-AAAAA-AAAGAG
*
16153 AAAATAAAAAGAAGA-
1 AAAATAAAAAAAAGAG
* * * * *
16168 AGAAGAAGAAAATGAA
1 AAAATAAAAAAAAGAG
* *
16184 AAAAAAAAGAAAAAGTG
1 AAAATAAA-AAAAAGAG
*
16201 AAAAAAGAAGAAAGAAGAAAG
1 AAAATA-AA-AAA-AAG--AG
* * *
16222 AAGAA-AGAGAAAAATAT
1 AA-AATA-AAAAAAAGAG
16239 AAAATAAAAAAAAGAG
1 AAAATAAAAAAAAGAG
16255 AAAATAAA
1 AAAATAAA
16263 GGGGGCTCAA
Statistics
Matches: 121, Mismatches: 27, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
15 11 0.09
16 35 0.29
17 35 0.29
18 24 0.20
19 5 0.04
20 3 0.02
21 6 0.05
22 2 0.02
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAATAAAAAAAAGAG
Found at i:17702 original size:55 final size:54
Alignment explanation
Indices: 17628--17941 Score: 343
Period size: 55 Copynumber: 5.7 Consensus size: 54
17618 TTTATGAAGA
* *
17628 TCGAGT-TCTATACTCTCTGATA-GAATAGAGAGCGGACCTGTTTGTTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGA-ACGAATAGGGAGCGGACC-GTTTGTTGAAGATTGT
* * *
17683 TCGAGT-TCTATACTCTCTGATA-GAATAGGGAGCGGACCCATTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGA-ACGAATAGGGAGCGGA-CCGTTTGTTGAAGATTGT
* * *
17738 TCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGAACCCATTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAACGAATAGGGAGCGGA-CCGTTTGTTGAAGATTGT
* *
17793 TCGAGTCTTATACTCCCTAAACGGAATAGGGAGCAGG-CACGTTTGCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAC-GAATAGGGAGC-GGAC-CGTTTGTTGAAGATTGT
* * * *
17849 TCAAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAATATTGT
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCGGAC-CGTTTGTTGAAGATTGT
*
17904 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACC
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCGGACC
17942 CGACTTTCGA
Statistics
Matches: 235, Mismatches: 17, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
54 3 0.01
55 183 0.78
56 48 0.20
57 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (54 bp):
TCGAGTCTTATACTCCCTGAACGAATAGGGAGCGGACCGTTTGTTGAAGATTGT
Found at i:17868 original size:111 final size:110
Alignment explanation
Indices: 17631--17940 Score: 362
Period size: 111 Copynumber: 2.8 Consensus size: 110
17621 ATGAAGATCG
* * * *
17631 AGTTCTATACTCTCTGATA-GAATAGAGAGCGGACCTGTTTGTTGAAGATTGTTCGAGT-TCTAT
1 AGTTCTATACTCCCTGA-ACGAATAGGGAGCGAACCCGTTTGTTGAAGATTGTTCGAGTCT-TAT
* * * * *
17694 ACTCTCTGATA-GAATAGGGAGCGGACCCATTTATTGAAGATTGTTCG
64 ACTCCCT-AAAGGAATAGGGAGCGGACACATTTACTGAAGATTGTTCA
* *
17741 AGTTCTATACTCCCTGAACGAATAGGGAGCGAACCCATTTATTGAAGATTGTTCGAGTCTTATAC
1 AGTTCTATACTCCCTGAACGAATAGGGAGCGAACCCGTTTGTTGAAGATTGTTCGAGTCTTATAC
* *
17806 TCCCTAAACGGAATAGGGAGCAGG-CACGTTTGCTGAAGATTGTTCA
66 TCCCTAAA-GGAATAGGGAGC-GGACACATTTACTGAAGATTGTTCA
* * *
17852 AG-TCTTATACTCCCTGAACGAATAGGGAGC-AGACACGTTTGCTGAATATTGTTCGAGTCTTAT
1 AGTTC-TATACTCCCTGAACGAATAGGGAGCGA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTAT
*
17915 ACTCCCTGAAGGAATAGGGAGCGGAC
64 ACTCCCTAAAGGAATAGGGAGCGGAC
17941 CCGACTTTCG
Statistics
Matches: 173, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
109 5 0.03
110 75 0.43
111 91 0.53
112 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (110 bp):
AGTTCTATACTCCCTGAACGAATAGGGAGCGAACCCGTTTGTTGAAGATTGTTCGAGTCTTATAC
TCCCTAAAGGAATAGGGAGCGGACACATTTACTGAAGATTGTTCA
Found at i:23369 original size:30 final size:30
Alignment explanation
Indices: 23335--23403 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
23325 AACACATATT
*
23335 CAAATCACATTAGTAAAGAGCATCATCAAC
1 CAAATCACATTAGTAAAGAGCAGCATCAAC
23365 CAAATCACATTAGTAAAGAGCAGCATCAAC
1 CAAATCACATTAGTAAAGAGCAGCATCAAC
23395 CAAATCACA
1 CAAATCACA
23404 ATCATCAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.48, C:0.25, G:0.10, T:0.17
Consensus pattern (30 bp):
CAAATCACATTAGTAAAGAGCAGCATCAAC
Found at i:30530 original size:15 final size:15
Alignment explanation
Indices: 30510--30541 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30500 TTCCTCCATT
30510 TCCCTCACTTTCCTC
1 TCCCTCACTTTCCTC
*
30525 TCCCTCTCTTTCCTC
1 TCCCTCACTTTCCTC
30540 TC
1 TC
30542 TTCTTCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (15 bp):
TCCCTCACTTTCCTC
Found at i:34405 original size:12 final size:12
Alignment explanation
Indices: 34383--34421 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34373 TTTTGGCTCC
*
34383 AGAGAGGCAGAG
1 AGAGAGACAGAG
*
34395 AGAGATACAGAG
1 AGAGAGACAGAG
*
34407 AGAGAGAGAGAG
1 AGAGAGACAGAG
34419 AGA
1 AGA
34422 TAGAGACTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.03
Consensus pattern (12 bp):
AGAGAGACAGAG
Found at i:34426 original size:12 final size:12
Alignment explanation
Indices: 34391--34427 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34381 CCAGAGAGGC
*
34391 AGAGAGAGATAC
1 AGAGAGAGATAG
34403 AGAGAGAG--AG
1 AGAGAGAGATAG
34413 AGAGAGAGATAG
1 AGAGAGAGATAG
34425 AGA
1 AGA
34428 CTTCACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.51, C:0.03, G:0.41, T:0.05
Consensus pattern (12 bp):
AGAGAGAGATAG
Found at i:38670 original size:2 final size:2
Alignment explanation
Indices: 38663--38730 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
38653 TCATGAAATA
* *
38663 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38705 AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38731 AGATACTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40788 original size:7 final size:7
Alignment explanation
Indices: 40776--40803 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
40766 CCAGCCTTTT
40776 CCTCTTC
1 CCTCTTC
40783 CCTCTTC
1 CCTCTTC
40790 CCTCTTC
1 CCTCTTC
40797 CCTCTTC
1 CCTCTTC
40804 TTATTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
CCTCTTC
Found at i:43607 original size:31 final size:31
Alignment explanation
Indices: 43538--43607 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
43528 TAATCCAGAT
* * *
43538 CGAGTATTATAAAAACCTATTATGGGATGAA
1 CGAGTACTACAAAAACCTATTATAGGATGAA
* * *
43569 CGGGTACTACAAAAGCCTATTATAGGATGAT
1 CGAGTACTACAAAAACCTATTATAGGATGAA
*
43600 TGAGTACT
1 CGAGTACT
43608 GCAGAGGCCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (31 bp):
CGAGTACTACAAAAACCTATTATAGGATGAA
Found at i:44648 original size:26 final size:25
Alignment explanation
Indices: 44593--44648 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
44583 CACTTCTATA
* *
44593 TAAA-CAATTAATCAAATCAGTTTT
1 TAAATCAACTAATCAAATCAGTTAT
44617 TCAAATCAACTAATCAAATCAGTTGAT
1 T-AAATCAACTAATCAAATCAGTT-AT
44644 TAAAT
1 TAAAT
44649 TAGCTACTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 3 0.11
26 21 0.78
27 2 0.07
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.34
Consensus pattern (25 bp):
TAAATCAACTAATCAAATCAGTTAT
Found at i:45614 original size:21 final size:21
Alignment explanation
Indices: 45563--45632 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
45553 TAAAACAACC
45563 ATTAAAT-TTATCAAATTATT
1 ATTAAATGTTATCAAATTATT
* *
45583 ATGAAGTTGTTATCAAATT-TT
1 ATTAA-ATGTTATCAAATTATT
* * *
45604 ATTAAACTGTTATGAAATAATC
1 ATTAAA-TGTTATCAAATTATT
45626 ATTAAAT
1 ATTAAAT
45633 CTATCGAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.10
21 18 0.46
22 17 0.44
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTAAATGTTATCAAATTATT
Found at i:45723 original size:32 final size:31
Alignment explanation
Indices: 45664--45742 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
45654 ATAACGTCAC
* * * *
45664 AATGATTATTTTGTAATAGTTCGATAAATTTT
1 AATGATTATTTTATAATAATTCAATAAA-TCT
* *
45696 AATGATTATTGTATAATAATTTAATAAATCT
1 AATGATTATTTTATAATAATTCAATAAATCT
*
45727 AATAATTATTTTATAA
1 AATGATTATTTTATAA
45743 ACTTTTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
AATGATTATTTTATAATAATTCAATAAATCT
Found at i:63747 original size:49 final size:50
Alignment explanation
Indices: 63672--63772 Score: 195
Period size: 49 Copynumber: 2.0 Consensus size: 50
63662 TTAGTTCTTA
63672 AAATATTATGTATATTTTTAATGGAACAATAAAATAAGGTAATATACTTT
1 AAATATTATGTATATTTTTAATGGAACAATAAAATAAGGTAATATACTTT
63722 AAATATTATGTAT-TTTTTAATGGAACAATAAAATAAGGTAATATACTTT
1 AAATATTATGTATATTTTTAATGGAACAATAAAATAAGGTAATATACTTT
63771 AA
1 AA
63773 TTGGAAAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 38 0.75
50 13 0.25
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.40
Consensus pattern (50 bp):
AAATATTATGTATATTTTTAATGGAACAATAAAATAAGGTAATATACTTT
Found at i:64601 original size:21 final size:21
Alignment explanation
Indices: 64577--64647 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
64567 ATGCAATACT
*
64577 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTAGAATAA
* * *
64598 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTAGAATAA
64619 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTAGAATAA
*
64640 ATTGCAAC
1 ATCGCAAC
64648 TCGAACTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 9 0.23
21 21 0.54
23 9 0.23
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTAGAATAA
Found at i:64638 original size:42 final size:42
Alignment explanation
Indices: 64574--64667 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 42
64564 CAAATGCAAT
*
64574 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG-
1 ACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTT-GA
* *
64616 ACTATCGCAACGAATTTAGAATAAATTGCAACTCGAACTTGA
1 ACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTGA
64658 ACTATCGCAA
1 ACTATCGCAA
64668 TTCGAATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (42 bp):
ACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTGA
Found at i:64814 original size:21 final size:20
Alignment explanation
Indices: 64752--64823 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
64742 ACTTCGACTA
*
64752 TCGCATTGCGATTTCCAAGT
1 TCGCATTGCGATGTCCAAGT
*
64772 TCGCATTGTGATGTCCAAGT
1 TCGCATTGCGATGTCCAAGT
*
64792 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGAT-GTCCAAGT
64813 TCGCATTGCGA
1 TCGCATTGCGA
64824 ATCTGGAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (20 bp):
TCGCATTGCGATGTCCAAGT
Found at i:70693 original size:29 final size:31
Alignment explanation
Indices: 70641--70707 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
70631 TAACTTATGC
*
70641 TTTTCTTTTCAGTTTAATATCTAACA-TTTA
1 TTTTATTTTCAGTTTAATATCTAACATTTTA
* * *
70671 TTTTATTTT-AGTTTAGTGTCTAATATTTTA
1 TTTTATTTTCAGTTTAATATCTAACATTTTA
70701 TTTTATT
1 TTTTATT
70708 ACTCAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.24, C:0.07, G:0.06, T:0.63
Consensus pattern (31 bp):
TTTTATTTTCAGTTTAATATCTAACATTTTA
Found at i:71172 original size:2 final size:2
Alignment explanation
Indices: 71165--71193 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71155 TCTTTTTAAA
71165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71194 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77430 original size:16 final size:16
Alignment explanation
Indices: 77405--77438 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
77395 TCACATTTTC
77405 ATATAAAAAAGTATGA
1 ATATAAAAAAGTATGA
*
77421 ATATAGAAAAGTATGA
1 ATATAAAAAAGTATGA
77437 AT
1 AT
77439 GAAACCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (16 bp):
ATATAAAAAAGTATGA
Found at i:79231 original size:21 final size:21
Alignment explanation
Indices: 79205--79246 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
79195 GTTACCCTTT
79205 CAACTTAAACCATTTTAAAGC
1 CAACTTAAACCATTTTAAAGC
* *
79226 CAACTTGAACCATTTTTAAGC
1 CAACTTAAACCATTTTAAAGC
79247 TGATTGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (21 bp):
CAACTTAAACCATTTTAAAGC
Found at i:81799 original size:20 final size:20
Alignment explanation
Indices: 81776--81866 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
81766 ACAGGTTCTA
*
81776 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGCGAATATGT
* ** *
81796 AAATCGCAATGATAAGATGT
1 AAATCGCAACGCGAATATGT
**
81816 AAATCGACATTGCGAATATGT
1 AAATCG-CAACGCGAATATGT
* *
81837 AAATCGCAACGCTAATTTGT
1 AAATCGCAACGCGAATATGT
81857 AAATCGCAAC
1 AAATCGCAAC
81867 ACATAAGTCA
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 41 0.72
21 16 0.28
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:81883 original size:20 final size:21
Alignment explanation
Indices: 81860--81907 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
81850 AATTTGTAAA
*
81860 TCGCAACACATAA-GTCAAAT
1 TCGCAACACAAAATGTCAAAT
*
81880 TCGCAACACAAAATTTCAAAT
1 TCGCAACACAAAATGTCAAAT
81901 TCGCAAC
1 TCGCAAC
81908 GCGATTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (21 bp):
TCGCAACACAAAATGTCAAAT
Found at i:81960 original size:40 final size:40
Alignment explanation
Indices: 81891--82093 Score: 169
Period size: 40 Copynumber: 4.9 Consensus size: 40
81881 CGCAACACAA
* * * * *
81891 AATTTCAAATTCGCAACGCGATTTTCTAATTCGCGACGCT
1 AATTTCGAATTCGCGACGCTAATTCCTAATTCGCGACGCT
* *
81931 AA-TTCGCGATTCGCGACGCTAATTCCTAATTCGCGATTCGCAACGC
1 AATTTCG-AATTCGCGACGCTAATTCCTAATTCGCGA--CG---C-T
* * * * *
81977 AATTTTGTAATTCGC-AGCGCGATTTTCTAATTCGTGACGCT
1 AATTTCG-AATTCGCGA-CGCTAATTCCTAATTCGCGACGCT
* *
82018 AATTTCGAATTCGCGACGCTAATTCCGAATTCGAGACGCT
1 AATTTCGAATTCGCGACGCTAATTCCTAATTCGCGACGCT
82058 AA-TTCTGAATTCGCGACGCTAATTCCTAATTCGCGA
1 AATTTC-GAATTCGCGACGCTAATTCCTAATTCGCGA
82094 TTCACAACGC
Statistics
Matches: 129, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
39 6 0.05
40 82 0.64
41 7 0.05
42 3 0.02
45 3 0.02
46 3 0.02
47 25 0.19
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (40 bp):
AATTTCGAATTCGCGACGCTAATTCCTAATTCGCGACGCT
Found at i:81962 original size:20 final size:20
Alignment explanation
Indices: 81916--82093 Score: 137
Period size: 20 Copynumber: 8.6 Consensus size: 20
81906 ACGCGATTTT
81916 CTAATTCGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTC
*
81936 GC-GATTCGCGACGCTAATTC
1 -CTAATTCGCGACGCTAATTC
* *
81956 CTAATTCGCGATTCGCAACGCAATTTT
1 CTAATTCGCGA--CG---C-TAA-TTC
* * * *
81983 GTAATTCGC-AGCGCGATTTT
1 CTAATTCGCGA-CGCTAATTC
* *
82003 CTAATTCGTGACGCTAATTT
1 CTAATTCGCGACGCTAATTC
*
82023 CGAATTCGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTC
* *
82043 CGAATTCGAGACGCTAATT-
1 CTAATTCGCGACGCTAATTC
82062 CTGAATTCGCGACGCTAATTC
1 CT-AATTCGCGACGCTAATTC
82083 CTAATTCGCGA
1 CTAATTCGCGA
82094 TTCACAACGC
Statistics
Matches: 128, Mismatches: 18, Indels: 23
0.76 0.11 0.14
Matches are distributed among these distances:
19 2 0.02
20 102 0.80
21 5 0.04
22 3 0.02
25 3 0.02
26 3 0.02
27 10 0.08
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (20 bp):
CTAATTCGCGACGCTAATTC
Found at i:81991 original size:27 final size:27
Alignment explanation
Indices: 81929--81980 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
81919 ATTCGCGACG
*
81929 CTAATTCGCGATTCGCGACGCTAATTC
1 CTAATTCGCGATTCGCAACGCTAATTC
81956 CTAATTCGCGATTCGCAACGC-AATT
1 CTAATTCGCGATTCGCAACGCTAATT
81981 TTGTAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (27 bp):
CTAATTCGCGATTCGCAACGCTAATTC
Found at i:82135 original size:20 final size:20
Alignment explanation
Indices: 82112--82160 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
82102 GCGATTTTGT
82112 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
**
82132 AATTCAAAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
*
82152 AATTAGGAA
1 AATTCGGAA
82161 CAAAACGGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (20 bp):
AATTCGGAATTAGCGTCGCG
Found at i:82219 original size:20 final size:20
Alignment explanation
Indices: 82196--82237 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
82186 GCGAACTCTA
82196 AATTCGCGAAGCTAATTCCG
1 AATTCGCGAAGCTAATTCCG
*
82216 AATTCGCGACGCTAATTCCG
1 AATTCGCGAAGCTAATTCCG
82236 AA
1 AA
82238 GTCACAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
AATTCGCGAAGCTAATTCCG
Found at i:82313 original size:20 final size:20
Alignment explanation
Indices: 82288--82375 Score: 149
Period size: 20 Copynumber: 4.4 Consensus size: 20
82278 TTACGAATTA
82288 CGAATTAGGAATTAGCATCG
1 CGAATTAGGAATTAGCATCG
82308 CGAATTAGGAATTAGCATCG
1 CGAATTAGGAATTAGCATCG
*
82328 CGAATTAGGAATTAGCGTCG
1 CGAATTAGGAATTAGCATCG
* *
82348 CGAATTCGGAATTAGCGTCG
1 CGAATTAGGAATTAGCATCG
82368 CGAATTAG
1 CGAATTAG
82376 AAAATAGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (20 bp):
CGAATTAGGAATTAGCATCG
Found at i:82485 original size:21 final size:21
Alignment explanation
Indices: 82461--82500 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
82451 ATTTACCTAT
82461 TCGCGTTACGAATTTGGAAAA
1 TCGCGTTACGAATTTGGAAAA
* *
82482 TCGCGTTGCGATTTTGGAA
1 TCGCGTTACGAATTTGGAA
82501 CCTGTGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
TCGCGTTACGAATTTGGAAAA
Found at i:82721 original size:21 final size:21
Alignment explanation
Indices: 82695--82736 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
82685 GTTACCCTTT
82695 CAACTTAAACCATGTTTAAGC
1 CAACTTAAACCATGTTTAAGC
* *
82716 CAACTTGAACCATTTTTAAGC
1 CAACTTAAACCATGTTTAAGC
82737 TGATTGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
CAACTTAAACCATGTTTAAGC
Found at i:84744 original size:20 final size:20
Alignment explanation
Indices: 84720--84772 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
84710 TTACCTTCTC
84720 ATTCTTCAATTTCTTATTTGT
1 ATTCTTCAATTTCTTATTT-T
*
84741 -TTCTTCAATCTCTTATTTT
1 ATTCTTCAATTTCTTATTTT
*
84760 ATTCTTCTATTTC
1 ATTCTTCAATTTC
84773 CTACAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTCTTCAATTTCTTATTTT
Found at i:102484 original size:22 final size:25
Alignment explanation
Indices: 102459--102522 Score: 62
Period size: 28 Copynumber: 2.6 Consensus size: 25
102449 AAAAAAGAGA
102459 AAAGAAAAAAAAA-A-A-ATTGTGC
1 AAAGAAAAAAAAAGAGAGATTGTGC
102481 AAAGGAAATAAAGAAAGAGAGATTGTGC
1 AAA-GAAA-AAA-AAAGAGAGATTGTGC
* *
102509 AATGAAGAAAAAAG
1 AAAGAAAAAAAAAG
102523 TTATATGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 3 0.09
25 7 0.21
26 4 0.12
27 4 0.12
28 9 0.26
ACGTcount: A:0.62, C:0.03, G:0.22, T:0.12
Consensus pattern (25 bp):
AAAGAAAAAAAAAGAGAGATTGTGC
Found at i:103359 original size:28 final size:28
Alignment explanation
Indices: 103307--103360 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
103297 CATACTTAGC
*
103307 ATAAAAATAAAACTTGAAAATAAAGAAA
1 ATAAAAATAAAACTTGAAAAGAAAGAAA
*
103335 ATAAAAA-AGAACTTGAAAAGGAAAGA
1 ATAAAAATAAAACTTGAAAA-GAAAGA
103361 GAAAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.15
Consensus pattern (28 bp):
ATAAAAATAAAACTTGAAAAGAAAGAAA
Found at i:106037 original size:28 final size:27
Alignment explanation
Indices: 106000--106069 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
105990 TTTTAAAATA
106000 ATTACCAGAATAGCACCAAAACAGAATT
1 ATTACCAGAATAGCACCAAAA-AGAATT
* * *
106028 ATTACCAGAATATCACTAAAATGAATT
1 ATTACCAGAATAGCACCAAAAAGAATT
*
106055 ATTTACTAGAATAGC
1 A-TTACCAGAATAGC
106070 CGGTCAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (27 bp):
ATTACCAGAATAGCACCAAAAAGAATT
Found at i:106089 original size:13 final size:13
Alignment explanation
Indices: 106071--106100 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
106061 TAGAATAGCC
106071 GGTCAACGGGTCG
1 GGTCAACGGGTCG
106084 GGTCAACGGGTCG
1 GGTCAACGGGTCG
106097 GGTC
1 GGTC
106101 GTGACCGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Done.